Selection and characterization of a DNA aptamer to crystal violet

Abstract

Aptamers are short single-stranded DNA or RNA, which can be selected in vitro by systematic evolution of ligands by exponential enrichment (SELEX). In order to develop novel light-up probes to substitute G-quadruplex (G4), we selected a DNA aptamer for crystal violet (CV), a triphenylmethane light-up dye, by a modified affinity chromatography-based SELEX. The ssDNA pool was first coupled on streptavidin-coated agarose beads through a biotin labeled complementary oligonucleotide, and then the aptamer sequences would be released from agarose beads by CV affinity. This method is simple, straightforward and effective. The aptamer sequence with a low micromolar dissociation constant (K_d) and good specificity was achieved after 11 rounds of selection. The light-up properties of the CV–aptamer were also investigated, and the CV showed dramatic fluorescence enhancement. The CV–aptamer pair could be further used as a novel light-up fluorescent probe to design biosensors.